In its frenzy to clear Iraq of Islamic State and erase any trace of the extremists' self-declared caliphate, Baghdad is running the risk of laying the foundation for the terror group's resurgence.

Human rights groups already have voiced repeated concerns about the treatment of civilians from areas once controlled by IS, and point to a growing anxiety among Iraqi Sunnis living under IS that they will be targeted no matter what.

"A large number of people have simply disappeared, who were picked up when they left ISIS," Donatella Rovera, Amnesty International's senior crisis response adviser, told VOA, using an acronym for the terror group.

"Pretty much everybody coming out of ISIS areas now is considered to have been there by choice and cooperated," she said.

FILE - Iraqi security forces and allied Sunni tribal fighters help trapped civilians cross from neighborhoods under control of the Islamic State group to neighborhoods under control of Iraqi security forces in Ramadi, 70 miles (115 kilometers) west of Baghdad, Iraq, Jan. 4, 2016.

Most of those who have vanished are believed to have been taken by Shi'ite militias that operate parallel to the Iraqi military with the blessing of the Baghdad government.

Males suspected to have collaborated with IS have disappeared from checkpoints — such as the Hezbollah-controlled point of Razazah, near Karbala — or from extrajudicial security screening centers run by Shi'ite militias near Fallujah.

And the fear is that human rights abuses and a lack of accountability will only increase as Iraqi federal forces, Kurdish Peshmerga and the coalition further tighten the noose around the IS stronghold of Mosul.

Fear of revenge

Although Shi'ite militias have stayed away from the Mosul front line so far, there are concerns they may move into the city as it falls to Iraqi forces.

"I fear that if the Shi'ite militias play a large role in Mosul, there will be significant revenge and retaliation actions, similar to what happened in Fallujah," said David Witty, a retired U.S. Army Special Forces colonel and former adviser to the Iraqi Counter Terrorism Service.

As Mosul falls, Iraqi officials increasingly will be forced to decide the fate of many of the more than 1 million civilians who have lived under IS rule for more than two years.

"There are questions as to whether the judicial system could cope with these numbers," said Francesco Motta, director of the office of human rights at the U.N. Assistance Mission for Iraq, or UNAMI.

FILE - Civilians flee villages outside Mosul a day after Iraqi Kurdish forces launched an operation east of the Islamic State-held city in Iraq, Aug. 15, 2016.

Failing system

Already, human rights groups say the system is failing.

In Anbar province, where the former IS-held cities of Ramadi and Fallujah are located, there are thousands of detainees with very few people conducting interrogations, low-quality lawyers, and few examining magistrates looking at cases, according to Amnesty's Rovera.

"Not only did they not have the expertise, the place was like a market house on a busy market day," Rovera said of one processing point that Amnesty visited.

"No one can do a good job in those circumstances, even if they had the skills," she added. "With the background of a dysfunctional judiciary, that does not give a good result.

"Hopefully, for Iraqi collaborators with IS, they will get turned over to the legal system, but many will probably not make it that far," Witty said.

Flood of suspects

Making the situation even more treacherous is the lack of resources dedicated to the official screening processes run by the Iraqi government and the Kurdish regional government.

FILE - Internally displaced civilians from Fallujah flee their homes during fighting between Iraqi security forces and Islamic State group during a military operation to regain control of the city, outside Fallujah, 40 miles (65 kilometers) west of Baghdad, Iraq.

Iraqis and foreign fighters suspected of affiliation or of fighting with IS will be transferred immediately to Ministry of Interior detention centers known as tasfiraat, or held in military prisons and charged under Iraq's counterterrorism laws.

The problem is there could be thousands of suspects. Tens of thousands of civilians already have fled IS-held areas, and an estimated 1 million additional civilians are in Mosul.

Women and children also may be found guilty.

"It is a concern that the families will be treated similarly to the fighters," Motta said. "The issue of accountability is becoming extremely important."

The U.N. has been advocating for an international tribunal or investigation mechanism and appropriate domestic mechanisms to be put in place to ensure that IS victims are not unfairly charged.

Motta also pointed out that IS fighters are not the only people guilty of crimes in the two-year conflict.

"Any attempt to limit jurisdiction to one party to the conflict, or to one particular group of victims or to one particular crime, would potentially be highly detrimental in terms of ensuring justice and promoting community reconciliation," he said.

If Sunni fears of sectarian abuses are realized, the future of Iraq could be bleak.

"At some point, four or five months down the road, six months down the road, a year down the road, when the governance is not being delivered, services are not being delivered, sectarian violence is taking place … [IS will] see an environment in which the conditions are ripe for them to re-establish themselves," warned Patrick Martin, Iraq research analyst with the Institute for the Study of War.

Sharon Behn is a foreign correspondent working out of Voice of America’s headquarters in Washington D.C Her current beat focuses on political, security and humanitarian developments in Iraq, Syria and Turkey. Follow Sharon on Twitter and on Facebook.